Known as the “Asian Water Tower”, the Tibetan Plateau (TP) is a rich water resource and serves an important ecological function. Climate change may cause changes to the water cycle, and these changes may affect the alpine vegetation growth. However, the variation characteristics of groundwater storage (GWS) and its driving factors and associated ecological effects in the TP are poorly understood. In this study, terrestrial water storage changes retrieved by GRACE (Gravity Recovery and Climate Experiment) were combined with GLDAS (Global Land Data Assimilation System) to estimate the GWS changes in the TP. The temporal and spatial variation characteristics of GWS were identified using linear regression and the modified Mann–Kendall (MMK) test, respectively. The analyses showed that the GWS of the TP decreased at an average rate of −0.89 mm/a from January 2003 to December 2021, but since January 2016, it gradually recovered at a rate of 1.47 mm/a. This shows that the GWS in the eastern and northern parts of the TP is decreasing, while the GWS in the western and southern parts is increasing. The influence of climate change on GWS in time and space was determined using the correlation analysis method. Decreased precipitation and permafrost degradation caused by increasing temperatures will lead to a decrease in GWS. On the other hand, rising temperatures may result in an increase in GWS in regions where glaciers are distributed. In this study, the ecological effects were represented by the relationship between GWS and vegetation change. A decline in GWS means that the vegetation will not receive enough water, leading to a decrease in the NDVI and the eventual degradation of grassland to sand, desert, or other kinds of unused land on the TP. On the other hand, an increase in GWS would promote vegetation restoration. The results of this study offer a new opportunity to reveal the groundwater changes in a cryosphere region and to assess the impact of changes in hydrological conditions on ecology.